Investigating the physiological and biochemical changes of ectothermic species before entering hibernation would contribute to the understanding of how they adapt to low-temperature environments. Here, red-eared slider turtle (Trachemys scripta elegans) hatchlings were maintained under different thermal treatments (24 °C, slowly decreasing temperatures from 24 °C to 14 °C, and to 4 °C). Hepatic metabolite alterations were measured to assess the metabolic impacts of low-temperature stress in this species. Of these differentially changed metabolites, some (e.g., raffinose, spermidine, allocholic acid, taurohyocholate, 2-ketobutyric acid, acetylcysteine) were shown to decrease, while others (e.g., stearolic acid, D-mannose) increased in low-temperature treatments. Our results indicated that short-term low-temperature stress might have limited impacts on lipid and energy metabolism in this species. The changes in other metabolites (e.g., allocholic acid, taurohyocholate, spermine, acetylcysteine) might be associated with a low food intake (and thus reduced digestive performance) and weakened immune ability of low-temperature-exposed animals.